1
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de Oliveira EB, Monteiro HF, Pereira JMV, Williams DR, Pereira RV, Silva Del Rio N, Menta PR, Machado VS, Lima FS. Changes in Uterine Metabolome Associated with Metritis Development and Cure in Lactating Holstein Cows. Metabolites 2023; 13:1156. [PMID: 37999252 PMCID: PMC10672899 DOI: 10.3390/metabo13111156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/26/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
The objective of this study was to identify alterations in the vaginal discharge (VD) metabolome and potential biomarkers to predict metritis development and a cure in dairy cows. This prospective cohort study was conducted on two dairies located in CA and TX. Vaginal discharge was evaluated and collected using the Metricheck® device. Cows were examined for metritis at 4, 7, and 9 days in milk (DIM). Cows with a fetid, watery, and reddish-brown uterine discharge were classified as having metritis and randomized to receive ceftiofur (n = 10) or remain untreated (n = 7). A cure was defined as the absence of a fetid, watery, reddish-brown uterine discharge at 14 d after enrollment. Vaginal discharge samples were collected from 86 cows within 6 h after parturition, at 4 and 7 DIM, at metritis diagnosis, and at 4 and 7 days after metritis diagnosis. Cows with metritis (MET; n = 17) were paired with counterparts without metritis (HTH) of a similar DIM and parity (n = 34). The uterine metabolome was evaluated using untargeted gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). Metabolomic data were analyzed using the MetaboAnalyst 5.0. Data were log-transformed and auto-scaled for normalization. Univariate analyses, including the fold-change, were performed to identify the metabolites linked to metritis development and its cure and principal component analysis and partial least squares discriminant analysis were performed to explain metabolite variance between animals developing or not developing metritis and being cured or not being cured of metritis. Comparing HTH with MET cows at calving, 12 metabolites were upregulated, and one was downregulated. At four and seven DIM, 51 and 74 metabolites, respectively, were altered between MET and HTH cows. After metritis development, three and five metabolites were upregulated in cows that were cured and in cows that received treatment and were cured, respectively. In all scenarios, the metabolites lignoceric, malic, and maleic acids, ornithine, and hypotaurine, which are associated with arginine/aminoacyl-tRNA biosynthesis and taurine/purine metabolism, were upregulated in HTH cows. Metritis was associated with changes in the uterine metabolome. Cows not being cured of metritis had changes in the uterus metabolome independent of receiving ceftiofur or remaining untreated. Metabolome analysis may be an important tool to understand the vaginal discharge changes during postpartum and the dynamics of metritis development and cures and help to identify biomarkers to predict metritis being cured.
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Affiliation(s)
- Eduardo B. de Oliveira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95106, USA; (E.B.d.O.); (H.F.M.); (R.V.P.); (N.S.D.R.)
- Veterinary Medicine Teaching and Research Center, Tulare, CA 93274, USA; (J.M.V.P.); (D.R.W.)
| | - Hugo F. Monteiro
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95106, USA; (E.B.d.O.); (H.F.M.); (R.V.P.); (N.S.D.R.)
| | - Jessica M. V. Pereira
- Veterinary Medicine Teaching and Research Center, Tulare, CA 93274, USA; (J.M.V.P.); (D.R.W.)
- Department of Animal Science, Federal University of Viçosa, Viçosa 36570-900, Brazil
| | - Deniece R. Williams
- Veterinary Medicine Teaching and Research Center, Tulare, CA 93274, USA; (J.M.V.P.); (D.R.W.)
| | - Richard V. Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95106, USA; (E.B.d.O.); (H.F.M.); (R.V.P.); (N.S.D.R.)
| | - Noelia Silva Del Rio
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95106, USA; (E.B.d.O.); (H.F.M.); (R.V.P.); (N.S.D.R.)
- Veterinary Medicine Teaching and Research Center, Tulare, CA 93274, USA; (J.M.V.P.); (D.R.W.)
| | - Paulo R. Menta
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX 79409, USA; (P.R.M.); (V.S.M.)
| | - Vinicius S. Machado
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX 79409, USA; (P.R.M.); (V.S.M.)
| | - Fabio S. Lima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95106, USA; (E.B.d.O.); (H.F.M.); (R.V.P.); (N.S.D.R.)
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2
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Parker DJ, Lalanne JB, Kimura S, Johnson GE, Waldor MK, Li GW. Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging. Cell Syst 2020; 11:121-130.e6. [PMID: 32726597 DOI: 10.1016/j.cels.2020.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 05/07/2020] [Accepted: 07/02/2020] [Indexed: 01/28/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) serve a dual role in charging tRNAs. Their enzymatic activities both provide protein synthesis flux and reduce uncharged tRNA levels. Although uncharged tRNAs can negatively impact bacterial growth, substantial concentrations of tRNAs remain deacylated even under nutrient-rich conditions. Here, we show that tRNA charging in Bacillus subtilis is not maximized due to optimization of aaRS production during rapid growth, which prioritizes demands in protein synthesis over charging levels. The presence of uncharged tRNAs is alleviated by precisely tuned translation kinetics and the stringent response, both insensitive to aaRS overproduction but sharply responsive to underproduction, allowing for just enough aaRS production atop a "fitness cliff." Notably, we find that the stringent response mitigates fitness defects at all aaRS underproduction levels even without external starvation. Thus, adherence to minimal, flux-satisfying protein production drives limited tRNA charging and provides a basis for the sensitivity and setpoints of an integrated growth-control network.
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Affiliation(s)
- Darren J Parker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Satoshi Kimura
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Grace E Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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3
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Eswarappa SM, Potdar AA, Sahoo S, Sankar S, Fox PL. Metabolic origin of the fused aminoacyl-tRNA synthetase, glutamyl-prolyl-tRNA synthetase. J Biol Chem 2018; 293:19148-19156. [PMID: 30309984 DOI: 10.1074/jbc.ra118.004276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/03/2018] [Indexed: 11/06/2022] Open
Abstract
About 1 billion years ago, in a single-celled holozoan ancestor of all animals, a gene fusion of two tRNA synthetases formed the bifunctional enzyme, glutamyl-prolyl-tRNA synthetase (EPRS). We propose here that a confluence of metabolic, biochemical, and environmental factors contributed to the specific fusion of glutamyl- (ERS) and prolyl- (PRS) tRNA synthetases. To test this idea, we developed a mathematical model that centers on the precursor-product relationship of glutamic acid and proline, as well as metabolic constraints on free glutamic acid availability near the time of the fusion event. Our findings indicate that proline content increased in the proteome during the emergence of animals, thereby increasing demand for free proline. Together, these constraints contributed to a marked cellular depletion of glutamic acid and its products, with potentially catastrophic consequences. In response, an ancient organism invented an elegant solution in which genes encoding ERS and PRS fused to form EPRS, forcing coexpression of the two enzymes and preventing lethal dysregulation. The substantial evolutionary advantage of this coregulatory mechanism is evidenced by the persistence of EPRS in nearly all extant animals.
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Affiliation(s)
- Sandeep M Eswarappa
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India,
| | - Alka A Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, and
| | - Sarthak Sahoo
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Santhosh Sankar
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
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4
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Growth-Rate Dependent Regulation of tRNA Level and Charging in Bacillus licheniformis. J Mol Biol 2017; 429:3102-3112. [DOI: 10.1016/j.jmb.2017.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/09/2017] [Accepted: 09/09/2017] [Indexed: 11/21/2022]
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5
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Núñez-Díaz JA, Fumanal M, Viguera E, Moriñigo MA, Balebona MC. Use of in vivo induced technology to identify antigens expressed by Photobacterium damselae subsp. piscicida during infection of Senegalese sole (Solea senegalensis). FISH & SHELLFISH IMMUNOLOGY 2017; 64:446-456. [PMID: 28359946 DOI: 10.1016/j.fsi.2017.03.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/22/2017] [Accepted: 03/26/2017] [Indexed: 06/07/2023]
Abstract
Photobacterium damselae subsp. piscicida (Phdp), the causative agent of photobacteriosis, is an important pathogen in marine aquaculture that affects many different fish species worldwide, including Solea senegalensis, an important fish species for aquaculture in the south of Europe. Bacteria express different repertoires of proteins in response to environmental conditions and when invading a host, sense in vivo environment and adapt by changing the expression of specific proteins. In the case of pathogens, identification of genes with up-regulated expression in vivo compared to in vitro conditions might give an insight into the genes relevant to the bacterial virulence. In the present work, in vivo induced antigen technology (IVIAT) has been used to search for Phdp genes only expressed or up-regulated in infected S. senegalensis. An expression library from Phdp was assayed against pooled sera from convalescent S. senegalensis specimens and 18 clones were positive, indicating that proteins encoded are expressed by Phdp during S. senegalensis infection and are immunogenic for this fish species. In addition, five proteins were reactive against adsorbed sera, indicating their in vivo induced character. Inosine-5'-monophosphate dehydrogenase, serine hydroxy methyltransferase and alanyl-tRNA synthethase, involved in aminoacid and nucleotide metabolism, the protein with antioxidant activity alkyl hydroperoxide reductase and a non-ribosomal peptide synthetase responsible for the synthesis of the siderophore piscibactin have been identified as antigens induced in Phdp during S. senegalensis infection. Proteins induced during in vivo growth of Phdp represent promising targets for the development of novel antimicrobial or prophylactic agents in the treatment and prevention of photobacteriosis.
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Affiliation(s)
- J A Núñez-Díaz
- Universidad de Málaga, Departamento de Microbiología, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - M Fumanal
- Universidad de Málaga, Departamento de Microbiología, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - E Viguera
- Universidad de Málaga, Área de Genética, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - M A Moriñigo
- Universidad de Málaga, Departamento de Microbiología, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - M C Balebona
- Universidad de Málaga, Departamento de Microbiología, Campus de Teatinos s/n, 29071 Málaga, Spain.
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6
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Ferro I, Chelysheva I, Ignatova Z. Competition for amino acid flux among translation, growth and detoxification in bacteria. RNA Biol 2017; 15:991-994. [PMID: 28296576 DOI: 10.1080/15476286.2017.1306174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Transfer-tRNAs (tRNAs) are central entities for translation that deliver amino acids to the ribosome to translate genetic information in an mRNA-template dependent manner. Recent discoveries from our laboratory show that in E. coli and B. licheniformis, some tRNAs are poorly charged despite the plentiful intracellular cognate amino acid. Specifically, tRNAs carrying amino acids that exert toxicity and inhibit bacterial growth when added separately to the growth medium are poorly charged. Here, we discuss various evolutionary strategies different bacterial cells have adopted to precisely hone the competition between amino acid utilization for translation and proliferation and combat the inhibitory effect toward maximizing bacterial fitness. These data add a new twist to the amino acid flux models and to our understanding of the complex intimate link between dynamics of translation and bacterial growth.
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Affiliation(s)
- Iolanda Ferro
- a Institute of Biochemistry and Molecular Biology, University of Hamburg , Germany
| | - Irina Chelysheva
- a Institute of Biochemistry and Molecular Biology, University of Hamburg , Germany
| | - Zoya Ignatova
- a Institute of Biochemistry and Molecular Biology, University of Hamburg , Germany
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7
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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8
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Duval M, Simonetti A, Caldelari I, Marzi S. Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics. Biochimie 2015; 114:18-29. [PMID: 25792421 DOI: 10.1016/j.biochi.2015.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/08/2015] [Indexed: 11/15/2022]
Abstract
To adapt their metabolism rapidly and constantly in response to environmental variations, bacteria often target the translation initiation process, during which the ribosome assembles on the mRNA. Here, we review different mechanisms of regulation mediated by cis-acting elements, sRNAs and proteins, showing, when possible, their intimate connection with the translational apparatus. Indeed the ribosome itself could play a direct role in several regulatory mechanisms. Different features of the regulatory signals (sequences, structures and their positions on the mRNA) are contributing to the large variety of regulatory mechanisms. Ribosome heterogeneity, variation of individual cells responses and the spatial and temporal organization of the translation process add more layers of complexity. This hampers to define manageable set of rules for bacterial translation initiation control.
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Affiliation(s)
- Mélodie Duval
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Angelita Simonetti
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
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9
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Henkin TM. The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:959-963. [PMID: 24816551 DOI: 10.1016/j.bbagrm.2014.04.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 12/23/2022]
Abstract
The T box riboswitch is a cis-acting regulatory RNA that controls expression of amino acid-related genes in response to the aminoacylation state of a specific tRNA. Multiple genes in the same organism can utilize this mechanism, with each gene responding independently to its cognate tRNA. The uncharged tRNA interacts directly with the regulatory RNA element, and this interaction promotes readthrough of an intrinsic transcriptional termination site upstream of the regulated coding sequence. A second class of T box elements uses a similar tRNA-dependent response to regulate translation initiation. This review will describe the current state of our knowledge about this regulatory system. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Tina M Henkin
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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10
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Stress responses of the industrial workhorse Bacillus licheniformis to osmotic challenges. PLoS One 2013; 8:e80956. [PMID: 24348917 PMCID: PMC3858371 DOI: 10.1371/journal.pone.0080956] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 11/19/2022] Open
Abstract
The Gram-positive endospore-forming bacterium Bacillus licheniformis can be found widely in nature and it is exploited in industrial processes for the manufacturing of antibiotics, specialty chemicals, and enzymes. Both in its varied natural habitats and in industrial settings, B. licheniformis cells will be exposed to increases in the external osmolarity, conditions that trigger water efflux, impair turgor, cause the cessation of growth, and negatively affect the productivity of cell factories in biotechnological processes. We have taken here both systems-wide and targeted physiological approaches to unravel the core of the osmostress responses of B. licheniformis. Cells were suddenly subjected to an osmotic upshift of considerable magnitude (with 1 M NaCl), and their transcriptional profile was then recorded in a time-resolved fashion on a genome-wide scale. A bioinformatics cluster analysis was used to group the osmotically up-regulated genes into categories that are functionally associated with the synthesis and import of osmostress-relieving compounds (compatible solutes), the SigB-controlled general stress response, and genes whose functional annotation suggests that salt stress triggers secondary oxidative stress responses in B. licheniformis. The data set focusing on the transcriptional profile of B. licheniformis was enriched by proteomics aimed at identifying those proteins that were accumulated by the cells through increased biosynthesis in response to osmotic stress. Furthermore, these global approaches were augmented by a set of experiments that addressed the synthesis of the compatible solutes proline and glycine betaine and assessed the growth-enhancing effects of various osmoprotectants. Combined, our data provide a blueprint of the cellular adjustment processes of B. licheniformis to both sudden and sustained osmotic stress.
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11
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Grigg JC, Ke A. Structural determinants for geometry and information decoding of tRNA by T box leader RNA. Structure 2013; 21:2025-32. [PMID: 24095061 PMCID: PMC3879790 DOI: 10.1016/j.str.2013.09.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/01/2013] [Accepted: 09/03/2013] [Indexed: 01/07/2023]
Abstract
T box riboswitches are cis-acting RNA elements that bind to tRNA and sense its aminoacylation state to influence gene expression. Here, we present the 3.2 Å resolution X-ray crystal structures of the T box Stem I-tRNA complex and tRNA, in isolation. T box Stem I forms an arched conformation with extensive intermolecular contacts to two key points of tRNA, the anticodon and D/T-loops. Free and complexed tRNA exist in significantly different conformations, with the contacts stabilizing flexible D/T-loops and a rearrangement of the D-loop. Using a designed T box RNA/tRNA system, we demonstrate that the T box riboswitch monitors the length and orientation of two essential contacts. Length or orientation mismatches engineered into the T box riboswitch and tRNA disrupt the complex, whereas simultaneous insertion of full helical turns realigns the interfaces and restores interaction between artificially elongated T box riboswitch and tRNA molecules.
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Affiliation(s)
- Jason C. Grigg
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14850, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14850, USA,Correspondence:
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12
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Abstract
The aminoacyl-tRNA synthetases (aaRSs) are essential components of the protein synthesis machinery responsible for defining the genetic code by pairing the correct amino acids to their cognate tRNAs. The aaRSs are an ancient enzyme family believed to have origins that may predate the last common ancestor and as such they provide insights into the evolution and development of the extant genetic code. Although the aaRSs have long been viewed as a highly conserved group of enzymes, findings within the last couple of decades have started to demonstrate how diverse and versatile these enzymes really are. Beyond their central role in translation, aaRSs and their numerous homologs have evolved a wide array of alternative functions both inside and outside translation. Current understanding of the emergence of the aaRSs, and their subsequent evolution into a functionally diverse enzyme family, are discussed in this chapter.
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13
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Abstract
Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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14
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Brill J, Hoffmann T, Putzer H, Bremer E. T-box-mediated control of the anabolic proline biosynthetic genes of Bacillus subtilis. Microbiology (Reading) 2011; 157:977-987. [DOI: 10.1099/mic.0.047357-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacillus subtilis possesses interlinked routes for the synthesis of proline. The ProJ–ProA–ProH route is responsible for the production of proline as an osmoprotectant, and the ProB–ProA–ProI route provides proline for protein synthesis. We show here that the transcription of the anabolic proBA and proI genes is controlled in response to proline limitation via a T-box-mediated termination/antitermination regulatory mechanism, a tRNA-responsive riboswitch. Primer extension analysis revealed mRNA leader transcripts of 270 and 269 nt for the proBA and proI genes, respectively, both of which are synthesized from SigA-type promoters. These leader transcripts are predicted to fold into two mutually exclusive secondary mRNA structures, forming either a terminator or an antiterminator configuration. Northern blot analysis allowed the detection of both the leader and the full-length proBA and proI transcripts. Assessment of the level of the proBA transcripts revealed that the amount of the full-length mRNA species strongly increased in proline-starved cultures. Genetic studies with a proB–treA operon fusion reporter strain demonstrated that proBA transcription is sensitively tied to proline availability and is derepressed as soon as cellular starvation for proline sets in. Both the proBA and the proI leader sequences contain a CCU proline-specific specifier codon prone to interact with the corresponding uncharged proline-specific tRNA. By replacing the CCU proline specifier codon in the proBA T-box leader with UUC, a codon recognized by a Phe-specific tRNA, we were able to synthetically re-engineer the proline-specific control of proBA transcription to a control that was responsive to starvation for phenylalanine.
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Affiliation(s)
- Jeanette Brill
- Philipps-University Marburg, Department of Biology, Laboratory for Microbiology, Karl-von-Frisch-Str. 8, D-35032 Marburg, Germany
| | - Tamara Hoffmann
- Philipps-University Marburg, Department of Biology, Laboratory for Microbiology, Karl-von-Frisch-Str. 8, D-35032 Marburg, Germany
| | - Harald Putzer
- CNRS UPR 9073 Insitut de Biologie Physico-Chimique (affiliated with Université de Paris 7 – Denis Diderot), 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Erhard Bremer
- Philipps-University Marburg, Department of Biology, Laboratory for Microbiology, Karl-von-Frisch-Str. 8, D-35032 Marburg, Germany
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15
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Jung S, Chun JY, Yim SH, Lee SS, Cheon CI, Song E, Lee MS. Transcriptional regulation of histidine biosynthesis genes in Corynebacterium glutamicum. Can J Microbiol 2010; 56:178-87. [DOI: 10.1139/w09-115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Corynebacterium glutamicum , a gram-positive bacterium, has been widely used for industrial amino acid production. Corynebacterium glutamicum his genes are located and transcribed in two unlinked loci, hisEG and hisDCB–orf1–orf2–hisHA–impA–hisFI. The latter his operon starts the transcription at the C residue localized 196 bp upstream of the hisD ATG start codon. Our computer-based sequence analysis showed that the region corresponding to the untranslated 5′ end of the transcript, named the hisD leader region, displays the typical features of the T-box transcriptional attenuation mechanism. Therefore, expression of the cat reporter gene under the control of the wild-type or mutated hisD leader regions was tested in multi-copy (pProm and pTer series) and in single-copy (pInt series) systems under conditions of sufficient or limited histidine. Our mutational studies led to the conclusion that the CAU histidine specifier and 5′-UGGA-3′ sequence in the hisD leader region are required for the hisDCB–orf1–orf2–hisHA–impA–hisFI gene regulation. The cat gene expression from the wild-type leader region was negatively regulated by histidine. However, the cat gene expression from mutated leader regions was irresponsive to the level of histidine in the growth medium. Taken together, we propose that a T-box mediated attenuation mechanism is responsible for the gene expression of the hisDCB–orf1–orf2–hisHA–impA–hisFI operon in C. glutamicum.
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Affiliation(s)
- Samil Jung
- Division of Biological Science and Research Center for Women’s Diseases, Sookmyung Women’s University, Seoul 140-742, Korea
- Samsung Advanced Institute of Technology, Suwon 440-600, Korea
| | - Jae-Yeon Chun
- Division of Biological Science and Research Center for Women’s Diseases, Sookmyung Women’s University, Seoul 140-742, Korea
- Samsung Advanced Institute of Technology, Suwon 440-600, Korea
| | - Sei-Heun Yim
- Division of Biological Science and Research Center for Women’s Diseases, Sookmyung Women’s University, Seoul 140-742, Korea
- Samsung Advanced Institute of Technology, Suwon 440-600, Korea
| | - Soo-Suk Lee
- Division of Biological Science and Research Center for Women’s Diseases, Sookmyung Women’s University, Seoul 140-742, Korea
- Samsung Advanced Institute of Technology, Suwon 440-600, Korea
| | - Choong-Il Cheon
- Division of Biological Science and Research Center for Women’s Diseases, Sookmyung Women’s University, Seoul 140-742, Korea
- Samsung Advanced Institute of Technology, Suwon 440-600, Korea
| | - Eunsook Song
- Division of Biological Science and Research Center for Women’s Diseases, Sookmyung Women’s University, Seoul 140-742, Korea
- Samsung Advanced Institute of Technology, Suwon 440-600, Korea
| | - Myeong-Sok Lee
- Division of Biological Science and Research Center for Women’s Diseases, Sookmyung Women’s University, Seoul 140-742, Korea
- Samsung Advanced Institute of Technology, Suwon 440-600, Korea
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16
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Green NJ, Grundy FJ, Henkin TM. The T box mechanism: tRNA as a regulatory molecule. FEBS Lett 2009; 584:318-24. [PMID: 19932103 DOI: 10.1016/j.febslet.2009.11.056] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 11/13/2009] [Accepted: 11/16/2009] [Indexed: 11/18/2022]
Abstract
The T box mechanism is widely used in Gram-positive bacteria to regulate expression of aminoacyl-tRNA synthetase genes and genes involved in amino acid biosynthesis and uptake. Binding of a specific uncharged tRNA to a riboswitch element in the nascent transcript causes a structural change in the transcript that promotes expression of the downstream coding sequence. In most cases, this occurs by stabilization of an antiterminator element that competes with formation of a terminator helix. Specific tRNA recognition by the nascent transcript results in increased expression of genes important for tRNA aminoacylation in response to decreased pools of charged tRNA.
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Affiliation(s)
- Nicholas J Green
- Department of Microbiology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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17
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Biochemical features and functional implications of the RNA-based T-box regulatory mechanism. Microbiol Mol Biol Rev 2009; 73:36-61. [PMID: 19258532 DOI: 10.1128/mmbr.00026-08] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The T-box mechanism is a common regulatory strategy used for modulating the expression of genes of amino acid metabolism-related operons in gram-positive bacteria, especially members of the Firmicutes. T-box regulation is usually based on a transcription attenuation mechanism in which an interaction between a specific uncharged tRNA and the 5' region of the transcript stabilizes an antiterminator structure in preference to a terminator structure, thereby preventing transcription termination. Although single T-box regulatory elements are common, double or triple T-box arrangements are also observed, expanding the regulatory range of these elements. In the present study, we predict the functional implications of T-box regulation in genes encoding aminoacyl-tRNA synthetases, proteins of amino acid biosynthetic pathways, transporters, and regulatory proteins. We also consider the global impact of the use of this regulatory mechanism on cell physiology. Novel biochemical relationships between regulated genes and their corresponding metabolic pathways were revealed. Some of the genes identified, such as the quorum-sensing gene luxS, in members of the Lactobacillaceae were not previously predicted to be regulated by the T-box mechanism. Our analyses also predict an imbalance in tRNA sensing during the regulation of operons containing multiple aminoacyl-tRNA synthetase genes or biosynthetic genes involved in pathways common to more than one amino acid. Based on the distribution of T-box regulatory elements, we propose that this regulatory mechanism originated in a common ancestor of members of the Firmicutes, Chloroflexi, Deinococcus-Thermus group, and Actinobacteria and was transferred into the Deltaproteobacteria by horizontal gene transfer.
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18
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Wels M, Groot Kormelink T, Kleerebezem M, Siezen RJ, Francke C. An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters. BMC Genomics 2008; 9:330. [PMID: 18625071 PMCID: PMC2494555 DOI: 10.1186/1471-2164-9-330] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 07/14/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND T-box anti-termination is an elegant and sensitive mechanism by which many bacteria maintain constant levels of amino acid-charged tRNAs. The amino acid specificity of the regulatory element is related to a so-called specifier codon and can in principle be used to guide the functional annotation of the genes controlled via the T-box anti-termination mechanism. RESULTS Hidden Markov Models were defined to search the T-box regulatory element and were applied to all completed prokaryotic genomes. The vast majority of the genes found downstream of the retrieved elements encoded functionalities related to transport and synthesis of amino acids and the charging of tRNA. This is completely in line with findings reported in literature and with the proposed biological role of the regulatory element. For several species, the functional annotation of a large number of genes encoding proteins involved in amino acid transport could be improved significantly on basis of the amino acid specificity of the identified T-boxes. In addition, these annotations could be extrapolated to a larger number of orthologous systems in other species. Analysis of T-box distribution confirmed that the element is restricted predominantly to species of the phylum Firmicutes. Furthermore, it appeared that the distribution was highly species specific and that in the case of amino acid transport some boxes seemed to "pop-up" only recently. CONCLUSION We have demonstrated that the identification of the molecular specificity of a regulatory element can be of great help in solving notoriously difficult annotation issues, e.g. by defining the substrate specificity of genes encoding amino acid transporters on basis of the amino acid specificity of the regulatory T-box. Furthermore, our analysis of the species-dependency of the occurrence of specific T-boxes indicated that these regulatory elements propagate in a semi-independent way from the genes that they control.
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Affiliation(s)
- Michiel Wels
- TI Food and Nutrition, Wageningen, The Netherlands.
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19
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A comparative proteomic analysis of Gluconacetobacter diazotrophicus PAL5 at exponential and stationary phases of cultures in the presence of high and low levels of inorganic nitrogen compound. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1578-89. [PMID: 18662807 DOI: 10.1016/j.bbapap.2008.06.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 06/07/2008] [Accepted: 06/23/2008] [Indexed: 11/23/2022]
Abstract
A proteomic view of G. diazotrophicus PAL5 at the exponential (E) and stationary phases (S) of cultures in the presence of low (L) and high levels (H) of combined nitrogen is presented. The proteomes analyzed on 2D-gels showed 131 proteins (42E+32S+29H+28L) differentially expressed by G. diazotrophicus, from which 46 were identified by combining mass spectrometry and bioinformatics tools. Proteins related to cofactor, energy and DNA metabolisms and cytoplasmic pH homeostasis were differentially expressed in E growth phase, under L and H conditions, in line with the high metabolic rate of the cells and the low pH of the media. Proteins most abundant in S-phase cells were stress associated and transporters plus transferases in agreement with the general phenomenon that binding protein-dependent systems are induced under nutrient limitation as part of hunger response. Cells grown in L condition produced nitrogen-fixation accessory proteins with roles in biosynthesis and stabilization of the nitrogenase complex plus proteins for protection of the nitrogenases from O(2)-induced inactivation. Proteins of the cell wall biogenesis apparatus were also expressed under nitrogen limitation and might function in the reshaping of the nitrogen-fixing G. diazotrophicus cells previously described. Genes whose protein products were detected in our analysis were mapped onto the chromosome and, based on the tendency of functionally related bacterial genes to cluster, we identified genes of particular pathways that could be organized in operons and are co-regulated. These results showed the great potential of proteomics to describe events in G. diazotrophicus cells by looking at proteins expressed under distinct growth conditions.
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20
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Vitreschak AG, Mironov AA, Lyubetsky VA, Gelfand MS. Comparative genomic analysis of T-box regulatory systems in bacteria. RNA (NEW YORK, N.Y.) 2008; 14:717-35. [PMID: 18359782 PMCID: PMC2271356 DOI: 10.1261/rna.819308] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 12/31/2007] [Indexed: 05/26/2023]
Abstract
T-box antitermination is one of the main mechanisms of regulation of genes involved in amino acid metabolism in Gram-positive bacteria. T-box regulatory sites consist of conserved sequence and RNA secondary structure elements. Using a set of known T-box sites, we constructed the common pattern and used it to scan available bacterial genomes. New T-boxes were found in various Gram-positive bacteria, some Gram-negative bacteria (delta-proteobacteria), and some other bacterial groups (Deinococcales/Thermales, Chloroflexi, Dictyoglomi). The majority of T-box-regulated genes encode aminoacyl-tRNA synthetases. Two other groups of T-box-regulated genes are amino acid biosynthetic genes and transporters, as well as genes with unknown function. Analysis of candidate T-box sites resulted in new functional annotations. We assigned the amino acid specificity to a large number of candidate amino acid transporters and a possible function to amino acid biosynthesis genes. We then studied the evolution of the T-boxes. Analysis of the constructed phylogenetic trees demonstrated that in addition to the normal evolution consistent with the evolution of regulated genes, T-boxes may be duplicated, transferred to other genes, and change specificity. We observed several cases of recent T-box regulon expansion following the loss of a previously existing regulatory system, in particular, arginine regulon in Clostridium difficile and methionine regulon in Lactobacillaceae. Finally, we described a new structural class of T-boxes containing duplicated terminator-antiterminator elements and unusual reduced T-boxes regulating initiation of translation in the Actinobacteria.
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MESH Headings
- 5' Untranslated Regions
- Amino Acid Transport Systems/genetics
- Amino Acid Transport Systems/metabolism
- Amino Acids/metabolism
- Bacteria/genetics
- Bacteria/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- DNA, Bacterial/genetics
- Evolution, Molecular
- Gene Expression Regulation, Bacterial
- Genome, Bacterial
- Genomics
- Models, Biological
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- Regulon
- Sequence Homology, Nucleic Acid
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
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Affiliation(s)
- Alexey G Vitreschak
- Institute for Information Transmission Problems (The Kharkevich Institute), Russian Academy of Sciences, Moscow 127994, Russia.
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21
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de Groot MJL, Daran-Lapujade P, van Breukelen B, Knijnenburg TA, de Hulster EAF, Reinders MJT, Pronk JT, Heck AJR, Slijper M. Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes. MICROBIOLOGY-SGM 2008; 153:3864-3878. [PMID: 17975095 DOI: 10.1099/mic.0.2007/009969-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Saccharomyces cerevisiae is unique among yeasts in its ability to grow rapidly in the complete absence of oxygen. S. cerevisiae is therefore an ideal eukaryotic model to study physiological adaptation to anaerobiosis. Recent transcriptome analyses have identified hundreds of genes that are transcriptionally regulated by oxygen availability but the relevance of this cellular response has not been systematically investigated at the key control level of the proteome. Therefore, the proteomic response of S. cerevisiae to anaerobiosis was investigated using metabolic stable-isotope labelling in aerobic and anaerobic glucose-limited chemostat cultures, followed by relative quantification of protein expression. Using independent replicate cultures and stringent statistical filtering, a robust dataset of 474 quantified proteins was generated, of which 249 showed differential expression levels. While some of these changes were consistent with previous transcriptome studies, many of the responses of S. cerevisiae to oxygen availability were, to our knowledge, previously unreported. Comparison of transcriptomes and proteomes from identical cultivations yielded strong evidence for post-transcriptional regulation of key cellular processes, including glycolysis, amino-acyl-tRNA synthesis, purine nucleotide synthesis and amino acid biosynthesis. The use of chemostat cultures provided well-controlled and reproducible culture conditions, which are essential for generating robust datasets at different cellular information levels. Integration of transcriptome and proteome data led to new insights into the physiology of anaerobically growing yeast that would not have been apparent from differential analyses at either the mRNA or protein level alone, thus illustrating the power of multi-level studies in yeast systems biology.
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Affiliation(s)
- Marco J L de Groot
- Netherlands Proteomics Centre, Utrecht, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
| | - Pascale Daran-Lapujade
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Bas van Breukelen
- Netherlands Proteomics Centre, Utrecht, The Netherlands
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
| | - Theo A Knijnenburg
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands
| | - Erik A F de Hulster
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Marcel J T Reinders
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands
| | - Jack T Pronk
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Albert J R Heck
- Netherlands Proteomics Centre, Utrecht, The Netherlands
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
| | - Monique Slijper
- Netherlands Proteomics Centre, Utrecht, The Netherlands
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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22
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Ryckelynck M, Giegé R, Frugier M. tRNAs and tRNA mimics as cornerstones of aminoacyl-tRNA synthetase regulations. Biochimie 2006; 87:835-45. [PMID: 15925436 DOI: 10.1016/j.biochi.2005.02.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Revised: 12/31/2004] [Accepted: 02/04/2005] [Indexed: 10/25/2022]
Abstract
Structural plasticity of transfer RNA (tRNA) molecules is essential for interactions with their biological partners in aminoacylation reactions and during ribosome-dependent protein synthesis. This holds true when tRNAs are recruited for other functions than translation. Here we review regulation pathways where tRNAs and tRNA mimics play a pivotal role. We further discuss the importance of the identity signals used in aminoacylation that are also required to specify regulatory mechanisms. Such mechanisms are diverse and intervene in transcription, splicing and translation. Altogether, the review highlights the many manners architectural features of tRNA were selected by evolution to control biological key processes.
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Affiliation(s)
- Michaël Ryckelynck
- Département Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15, rue René Descartes, F-67084 Strasbourg cedex, France
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23
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Morbach S, Junger C, Sahm H, Eggeling L. Attenuation control of ilvBNC in Corynebacterium glutamicum: evidence of leader peptide formation without the presence of a ribosome binding site. J Biosci Bioeng 2005; 90:501-7. [PMID: 16232899 DOI: 10.1016/s1389-1723(01)80030-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2000] [Accepted: 08/01/2000] [Indexed: 11/25/2022]
Abstract
The ilvBNC operon of Corynebacterium glutamicum encodes acetohydroxy acid synthase and isomero-reductase, which are key enzymes of L-isoleucine, L-valine and L-leucine syntheses. In this study we identified the transcript initiation site of ilvBNC operon 292 nucleotides in front of the first structural gene, and detected the formation of a short transcript from the leader region in addition to the full-length transcript of the operon. This identifies the control of ilvBNC transcription by an attenuation mechanism involving antitermination. Mutations in the leader region were made and their effect on the operon expression in ilvB'lacZ fusions was quantified. Although a presumed leader-peptide-coding region is only one nucleotide away from the transcript initiation site determined, there is clear evidence to support the formation of this leader peptide: (i) the substitution of initiation codon ATG of the peptide by AGG reduced lacZ expression of the appropriate fusion construct to 19%; (ii) the replacement of three subsequent Val codons by Ala codons resulted in the loss of Val-dependent expression; and (iii) a leader peptide LacZ fusion resulted in active beta-galactosidase. Based on these results, it is concluded that transcription of ilvBNC is controlled by a translational-coupled attenuation mechanism. The absence of a ribosome binding site for leader peptide formation means that additional mechanisms may contribute to the transcription control at the decoding initiation step in the leader peptide formation.
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Affiliation(s)
- S Morbach
- Institut für Biochemie der Universität zu Köln, Zülpicher Str. 47, 50674 Köln, Germany
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24
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Even S, Pellegrini O, Zig L, Labas V, Vinh J, Bréchemmier-Baey D, Putzer H. Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E. Nucleic Acids Res 2005; 33:2141-52. [PMID: 15831787 PMCID: PMC1079966 DOI: 10.1093/nar/gki505] [Citation(s) in RCA: 243] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many prokaryotic organisms lack an equivalent of RNase E, which plays a key role in mRNA degradation in Escherichia coli. In this paper, we report the purification and identification by mass spectrometry in Bacillus subtilis of two paralogous endoribonucleases, here named RNases J1 and J2, which share functional homologies with RNase E but no sequence similarity. Both enzymes are able to cleave the B.subtilis thrS leader at a site that can also be cleaved by E.coli RNase E. We have previously shown that cleavage at this site increases the stability of the downstream messenger. Moreover, RNases J1/J2 are sensitive to the 5′ phosphorylation state of the substrate in a site-specific manner. Orthologues of RNases J1/J2, which belong to the metallo-β-lactamase family, are evolutionarily conserved in many prokaryotic organisms, representing a new family of endoribonucleases. RNases J1/J2 appear to be implicated in regulatory processing/maturation of specific mRNAs, such as the T-box family members thrS and thrZ, but may also contribute to global mRNA degradation.
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Affiliation(s)
| | | | | | - Valerie Labas
- CNRS UMR7637, ESPCI10 rue Vauquelin 75005 Paris, France
| | - Joelle Vinh
- CNRS UMR7637, ESPCI10 rue Vauquelin 75005 Paris, France
| | | | - Harald Putzer
- To whom correspondence should be addressed. Tel: +33 1 58 41 51 27; Fax: +33 1 58 41 50 20;
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25
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Yousef MR, Grundy FJ, Henkin TM. Structural transitions induced by the interaction between tRNA(Gly) and the Bacillus subtilis glyQS T box leader RNA. J Mol Biol 2005; 349:273-87. [PMID: 15890195 DOI: 10.1016/j.jmb.2005.03.061] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 03/18/2005] [Accepted: 03/22/2005] [Indexed: 10/25/2022]
Abstract
The T box system regulates expression of amino acid-related genes in Gram-positive bacteria through premature termination of transcription. Synthesis of the full-length mRNA requires stabilization of an antiterminator element in the 5' untranslated leader RNA by the cognate uncharged tRNA. tRNA(Gly)-dependent antitermination of the Bacillus subtilis glyQS gene (encoding glycyl-tRNA synthetase) can be reproduced in a purified in vitro transcription system, indicating that the nascent transcript is sufficient for interaction with the tRNA. Genetic analyses previously demonstrated base pairing of a single codon in the leader RNA with the tRNA anticodon, and between the antiterminator and the tRNA acceptor end. In this study, we established conditions for specific binding of tRNA(Gly) to glyQS leader RNA generated by phage T7 RNA polymerase. Structural mapping studies revealed tRNA(Gly)-induced protection in the glyQS leader RNA at the two known sites of interaction with the tRNA, as well as at other regions between these sites. The proposed tRNA-dependent structural switch between the competing terminator and antiterminator forms of the leader RNA was demonstrated directly. Changes in tRNA(Gly) upon binding to glyQS leader RNA were detected in the anticodon loop, consistent with pairing with the specifier sequence, and in the highly conserved G19 in the D-loop, similar to effects induced by codon-anticodon interaction in the ribosome. This study provides biochemical evidence for direct interaction of tRNA(Gly) with full-length in vitro transcribed glyQS leader RNA, and an initial view of structural modulations of both RNA partners within the complex.
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MESH Headings
- 5' Untranslated Regions/chemistry
- 5' Untranslated Regions/genetics
- 5' Untranslated Regions/metabolism
- Bacillus subtilis/genetics
- Glycine-tRNA Ligase/genetics
- Magnesium/pharmacology
- Nucleic Acid Conformation
- Peptide Chain Termination, Translational/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Gly/chemistry
- RNA, Transfer, Gly/genetics
- RNA, Transfer, Gly/metabolism
- Ribonuclease H/metabolism
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Affiliation(s)
- Mary R Yousef
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
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26
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Yousef MR, Grundy FJ, Henkin TM. tRNA requirements for glyQS antitermination: a new twist on tRNA. RNA (NEW YORK, N.Y.) 2003; 9:1148-1156. [PMID: 12923262 PMCID: PMC1370478 DOI: 10.1261/rna.5540203] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2003] [Accepted: 05/30/2003] [Indexed: 05/24/2023]
Abstract
Transcription antitermination of the Bacillus subtilis glyQS gene, a member of the T box gene regulation family, can be induced during in vitro transcription in a minimal system using purified B. subtilis RNA polymerase by the addition of unmodified T7 RNA polymerase-transcribed tRNA(Gly). Antitermination was previously shown to depend on base-pairing between the glyQS leader and the tRNA at the anticodon and acceptor ends. In this study, variants of tRNA(Gly) were generated to identify additional tRNA elements required for antitermination activity, and to determine the effect of structural changes in the tRNA. We find that additions to the 3' end of the tRNA blocked antitermination, in agreement with the prediction that uncharged tRNA is the effector in vivo, whereas insertion of 1 nucleotide between the acceptor stem and the 3' UCCA residues had no effect. Disruption of the D-loop/T-loop tertiary interaction inhibited antitermination function, as was previously demonstrated for tRNA(Tyr)-directed antitermination of the B. subtilis tyrS gene in vivo. Insertion of a single base pair in the anticodon stem was tolerated, whereas further insertions abolished antitermination. However, we find that major alterations in the length of the acceptor stem are tolerated, and the insertions exhibited a pattern of periodicity suggesting that there is face-of-the-helix dependence in the positioning of the unpaired UCCA residues at the 3' end of the tRNA for interaction with the antiterminator bulge and antitermination.
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Affiliation(s)
- Mary R Yousef
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
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27
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Abstract
Dimeric class II aspartyl-tRNA synthetase (AspRS) from yeast has a modular architecture and includes an N-terminal appendix of 70 amino acid residues that protrudes from the anticodon-binding module. This extension, of predicted helical structure, is not essential for aminoacylation but contains an RNA-binding motif that promotes non-specific interactions with tRNAs. As shown here, this protein extension can also interact with the 5' end of the AspRS mRNA. In vitro, optimal binding occurs on an mRNA domain comprising part of the 87 nucleotide long 5'UTR and the sequence encoding the N-terminal appendix. At the protein side, only the appendix and the anticodon-binding module participate in the interaction between AspRS and the mRNA domain. Binding is specific, since only tRNA(Asp) can dissociate the complex. In vivo, AspRS also binds specifically this mRNA domain and in doing so triggers a reduced translation of a fused GFP mRNA. From that, a mechanism for the regulation of this eukaryotic aminoacyl-tRNA synthetase is proposed. Implications for aspartylation accuracy in yeast are given.
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Affiliation(s)
- Magali Frugier
- Département "Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse", UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
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28
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Abstract
This review focuses on the enzymes and pathways of RNA processing and degradation in Bacillus subtilis, and compares them to those of its gram-negative counterpart, Escherichia coli. A comparison of the genomes from the two organisms reveals that B. subtilis has a very different selection of RNases available for RNA maturation. Of 17 characterized ribonuclease activities thus far identified in E. coli and B. subtilis, only 6 are shared, 3 exoribonucleases and 3 endoribonucleases. Some enzymes essential for cell viability in E. coli, such as RNase E and oligoribonuclease, do not have homologs in B. subtilis, and of those enzymes in common, some combinations are essential in one organism but not in the other. The degradation pathways and transcript half-lives have been examined to various degrees for a dozen or so B. subtilis mRNAs. The determinants of mRNA stability have been characterized for a number of these and point to a fundamentally different process in the initiation of mRNA decay. While RNase E binds to the 5' end and catalyzes the rate-limiting cleavage of the majority of E. coli RNAs by looping to internal sites, the equivalent nuclease in B. subtilis, although not yet identified, is predicted to scan or track from the 5' end. RNase E can also access cleavage sites directly, albeit less efficiently, while the enzyme responsible for initiating the decay of B. subtilis mRNAs appears incapable of direct entry. Thus, unlike E. coli, RNAs possessing stable secondary structures or sites for protein or ribosome binding near the 5' end can have very long half-lives even if the RNA is not protected by translation.
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Affiliation(s)
- Ciarán Condon
- UPR 9073, Institut de Biologie Physico-Chimique, 75005 Paris, France.
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29
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Putzer H, Condon C, Brechemier-Baey D, Brito R, Grunberg-Manago M. Transfer RNA-mediated antitermination in vitro. Nucleic Acids Res 2002; 30:3026-33. [PMID: 12136084 PMCID: PMC135736 DOI: 10.1093/nar/gkf415] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The threonyl-tRNA synthetase gene (thrS) is a member of the T-box family of approximately 250 genes, found essentially in Gram-positive bacteria, regulated by a tRNA-dependent antitermination mechanism in response to starvation for the cognate amino acid. While interaction between uncharged tRNA and the untranslated leader region of these genes has been firmly established by genetic means, attempts to show this interaction or to reconstitute the antitermination mechanism in vitro using purified tRNAs have so far failed. In addition, a number of conserved sequences have been identified in the T-box leaders, for which no function has yet been assigned. This suggests that factors other than the tRNA are important for this type of control. Here we demonstrate tRNA-mediated antitermination for the first time in vitro, using the regulatory tRNA(Thr) isoacceptor isolated from Bacillus subtilis and a partially purified protein fraction. As predicted by the model, aminoacylation of tRNA(Thr(GGU)) with threonine completely abolishes its ability to act as an effector. The role of the partially purified protein fraction can be functionally substituted by high concentrations of spermidine. However, this polyamine does not play a significant role in the induction of thrS expression in vivo, suggesting that it is specific protein co-factors that promote T-box gene regulation in conjunction with uncharged tRNA.
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MESH Headings
- Anticodon/genetics
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Bacterial Proteins/genetics
- Exotoxins
- Membrane Proteins/genetics
- Mutation
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Thr/genetics
- RNA, Transfer, Thr/metabolism
- Terminator Regions, Genetic/genetics
- Threonine-tRNA Ligase/genetics
- Threonine-tRNA Ligase/metabolism
- Transcription, Genetic/genetics
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Affiliation(s)
- Harald Putzer
- CNRS-UPR 9073, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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30
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Becker P, Hufnagle W, Peters G, Herrmann M. Detection of differential gene expression in biofilm-forming versus planktonic populations of Staphylococcus aureus using micro-representational-difference analysis. Appl Environ Microbiol 2001; 67:2958-65. [PMID: 11425708 PMCID: PMC92967 DOI: 10.1128/aem.67.7.2958-2965.2001] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial proliferation and biofilm formation on biologic or inert substrates are characteristics of invasive Staphylococcus aureus infections and is associated with phenotypic alterations such as reduced antimicrobial susceptibility. To identify genes which are typically expressed in biofilms, a micro-representational-difference analysis (micro-RDA) was adapted for gram-positive bacteria and used with cDNA derived from populations of S. aureus DSM 20231 growing in a biofilm or plankonically. In comparison to previously described cDNA RDA protocols, micro-RDA has the advantages that only minimal quantities of total RNA are needed and, most importantly, that total RNA can be used since the large amount of rRNA in total RNA does not interfere with the micro-RDA procedure. Using a series of spiked controls with various amounts of MS2 RNA in a background of total RNA from S. aureus, the equivalent of five copies of MS2 per cell were detectable after three rounds of subtractive enrichment. Five genes were identified as being differentially expressed in biofilm versus planktonic cultures. These genes revealed homology to a threonyl-tRNA synthetase, a phosphoglycerate mutase, a triosephosphate isomerase, an alcohol dehydrogenase I, and a ClpC ATPase. Differential levels of expression were subsequently confirmed by standard Northern blotting. In conclusion, micro-RDA is a sensitive and specific method to detect transcripts differentially expressed as a function of different S. aureus growth conditions.
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Affiliation(s)
- P Becker
- Department of Medical Microbiology, University of Münster, Münster, Germany.
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31
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van de Guchte M, Ehrlich SD, Chopin A. Identity elements in tRNA-mediated transcription antitermination: implication of tRNA D- and T-arms in mRNA recognition. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1223-1233. [PMID: 11320125 DOI: 10.1099/00221287-147-5-1223] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
tRNA-mediated transcription antitermination has been shown to control the expression of several amino acid biosynthesis operons and aminoacyl-tRNA-synthetase-encoding genes in Gram-positive bacteria. A model originally put forward by Grundy & Henkin describes the conserved structural features of the leader sequences of these operons and genes. Two sequences of 3 and 4 nt, respectively, take a central position in this model and are thought to be responsible for the binding of the system-specific uncharged tRNA, an interaction which would stabilize the antiterminator conformation of the leader. Here a further evolution of this model is presented based on an analysis of trp regulation in Lactococcus lactis in which a function is assigned to hitherto unexplained conserved structures in the leader sequence. It is postulated that the mRNA-tRNA interaction involves various parts of the tRNA in addition to the anticodon and the acceptor in the original model and that these additional interactions contribute to the recognition of a specific tRNA, and hence to the specificity and efficacy of the regulatory response.
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Affiliation(s)
- Maarten van de Guchte
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, 78352Jouy-en-Josas Cedex, France1
| | - S Dusko Ehrlich
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, 78352Jouy-en-Josas Cedex, France1
| | - Alain Chopin
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, 78352Jouy-en-Josas Cedex, France1
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32
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Pelchat M, Lapointe J. Aminoacyl-tRNA synthetase genes of Bacillus subtilis: organization and regulation. Biochem Cell Biol 1999. [DOI: 10.1139/o99-040] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In Bacillus subtilis, 14 of the 24 genes encoding aminoacyl-tRNA synthetases (aaRS) are regulated by tRNA-mediated antitermination in response to starvation for their cognate aminoacid. Their transcripts have an untranslated leader mRNA of about 300 nucleotides, including alternative and mutually exclusive terminator-antiterminator structures, just upstream from the translation initiation site. Following antitermination, some of these transcripts are cleaved leaving at the 5prime-end of the mature mRNAs, stable secondary structures that can protect them against degradation. Although most B. subtilis aaRS genes are expressed as monocistronic mRNAs, the gltX gene encoding the glutamyl-tRNA synthetase is cotranscribed with cysE and cysS encoding serine acetyl-transferase and cysteinyl-tRNA synthetase, respectively. Transcription of gltX is not controlled by a tRNA, but tRNACys-mediated antitermination regulates the elongation of transcription into cysE and cysS. The full-length gltX-cysE-cysS transcript is then cleaved into a monocistronic gltX mRNA and a cysE-cysS mRNA.Key words: regulation, aminoacyl-tRNA synthetase, T-Box, processing.
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33
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Sissler M, Delorme C, Bond J, Ehrlich SD, Renault P, Francklyn C. An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis. Proc Natl Acad Sci U S A 1999; 96:8985-90. [PMID: 10430882 PMCID: PMC17719 DOI: 10.1073/pnas.96.16.8985] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In addition to their essential catalytic role in protein biosynthesis, aminoacyl-tRNA synthetases participate in numerous other functions, including regulation of gene expression and amino acid biosynthesis via transamidation pathways. Herein, we describe a class of aminoacyl-tRNA synthetase-like (HisZ) proteins based on the catalytic core of the contemporary class II histidyl-tRNA synthetase whose members lack aminoacylation activity but are instead essential components of the first enzyme in histidine biosynthesis ATP phosphoribosyltransferase (HisG). Prediction of the function of HisZ in Lactococcus lactis was assisted by comparative genomics, a technique that revealed a link between the presence or the absence of HisZ and a systematic variation in the length of the HisG polypeptide. HisZ is required for histidine prototrophy, and three other lines of evidence support the direct involvement of HisZ in the transferase function. (i) Genetic experiments demonstrate that complementation of an in-frame deletion of HisG from Escherichia coli (which does not possess HisZ) requires both HisG and HisZ from L. lactis. (ii) Coelution of HisG and HisZ during affinity chromatography provides evidence of direct physical interaction. (iii) Both HisG and HisZ are required for catalysis of the ATP phosphoribosyltransferase reaction. This observation of a common protein domain linking amino acid biosynthesis and protein synthesis implies an early connection between the biosynthesis of amino acids and proteins.
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Affiliation(s)
- M Sissler
- Department of Biochemistry, College of Medicine, Given Building, University of Vermont, Burlington, VT 05405, USA
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34
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Delorme C, Ehrlich SD, Renault P. Regulation of expression of the Lactococcus lactis histidine operon. J Bacteriol 1999; 181:2026-37. [PMID: 10094678 PMCID: PMC93613 DOI: 10.1128/jb.181.7.2026-2037.1999] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Lactococcus lactis, the his operon contains all the genes necessary for histidine biosynthesis. It is transcribed from a unique promoter, localized 300 bp upstream of the first gene. The region corresponding to the untranslated 5' end of the transcript, named the his leader region, displays the typical features of the T box transcriptional attenuation mechanism which is involved in the regulation of many amino acid biosynthetic operons and tRNA synthetase genes in gram-positive bacteria. Here we describe the regulation of transcription of the his operon by the level of histidine in the growth medium. In the absence of histidine, two transcripts are present. One covers the entire operon, while the other stops at a terminator situated about 250 bp downstream of the transcription start point. DNA sequences implicated in regulation of the his operon were identified by transcriptional fusion with luciferase genes and site-directed mutagenesis. In addition to the previously defined sequences necessary for effective T-box-mediated regulation, new essential regions were identified. Eighteen percent of the positions of the his leader region were found to differ in seven distantly related strains of L. lactis. Analysis of the variable positions supports the folding model of the central part of the his leader region. Lastly, in addition to the T-box-mediated regulation, the operon is regulated at the level of initiation of transcription, which is repressed in the presence of histidine. An operator site, necessary for full repression, overlaps the terminator involved in the T box attenuation mechanism. The functionality of the operator is altered on plasmids with low and high copy numbers, suggesting that supercoiling may play a role in the expression of the his operon. The extents of regulation at the levels of initiation and attenuation of transcription are 6- to 8-fold and 14-fold, respectively. Together, the two levels of control allow a 120-fold range of regulation of the L. lactis operon by histidine.
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Affiliation(s)
- C Delorme
- Laboratoire de Génétique Microbienne, Institut National de Recherche Agronomique, 78352 Jouy-en-Josas Cedex, France.
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35
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Luo D, Condon C, Grunberg-Manago M, Putzer H. In vitro and in vivo secondary structure probing of the thrS leader in Bacillus subtilis. Nucleic Acids Res 1998; 26:5379-87. [PMID: 9826762 PMCID: PMC148014 DOI: 10.1093/nar/26.23.5379] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Bacillus subtilis thrS gene is a member of the T-box gene family in Gram-positive organisms whose expression is regulated by a tRNA-mediated transcriptional antitermination mechanism involving a direct tRNA:mRNA interaction. The complex leader sequences of these genes share only short stretches of primary sequence homology, but a common secondary structure has been proposed by comparing the leaders of many genes of this family. The proposed mechanism forthe tRNA:mRNA interaction depends heavily on the secondary structure model, but is so far only supported by genetic evidence. We have studied the structure of the B.subtilis thrS leader in solution, in protection experiments using both chemical and enzymatic probes. The thrS leader structure was also probed in vivo using dimethylsulphate and the in vitro and in vivo data are in good accordance. We have organized the thrS leader into three major domains comprising six separate stem-loops. All but one of the short sequences conserved in this gene family are present in loop structures. The ACC specifier codon proposed to interact with the tRNAThrGGUisoacceptor is present in a bulge and probably exists in a stacking conformation. The proposed antiterminator structure is not visible in transcripts containing the terminator, but was probed using a transcript with the 3'-half of the terminator deleted and its folding appears consistent with the regulatory model. The leader sequences, and in particular the specifier domains, of the other genes of this family can be folded similarly to the experimentally solved thrS structure.
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Affiliation(s)
- D Luo
- UPR 9073, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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36
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Frenkiel H, Bardowski J, Ehrlich SD, Chopin A. Transcription of the trp operon in Lactococcus lactis is controlled by antitermination in the leader region. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 8):2103-2111. [PMID: 9720031 DOI: 10.1099/00221287-144-8-2103] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The regulatory functions of the leader region preceding the Lactococcus lactis trp operon have been studied by mutagenesis analysis. This leader presents striking similarity to 'T-box' leaders found upstream of many Gram-positive aminoacyl-tRNA synthetase genes and some amino acid biosynthesis operons, which are controlled by antitermination through interaction of the leader transcript with cognate uncharged tRNA. A region of the L. lactis leader transcript also contains a series of (G/U) AG repeats which, in Bacillus, are involved in the binding of the trp RNA-binding protein (TRAP) which controls trp transcription. A screen was developed for the isolation of regulatory mutants affected in the leader region. All spontaneous mutants contained deletions; point mutations were only obtained after UV-induced mutagenesis. All mutations affected the putative transcription terminator upstream of the trp operon, demonstrating that trp is indeed controlled by transcription antitermination.
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Affiliation(s)
- HéléeGne Frenkiel
- Laboratoire de Génètique Microbienne, Institut National de la Recherche Agronomique78352 Jouy-en-Josas CedexFrance
| | - Jacek Bardowski
- Laboratoire de Génètique Microbienne, Institut National de la Recherche Agronomique78352 Jouy-en-Josas CedexFrance
| | - S Dusko Ehrlich
- Laboratoire de Génètique Microbienne, Institut National de la Recherche Agronomique78352 Jouy-en-Josas CedexFrance
| | - Alain Chopin
- Laboratoire de Génètique Microbienne, Institut National de la Recherche Agronomique78352 Jouy-en-Josas CedexFrance
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37
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Dekkers LC, van der Bij AJ, Mulders IH, Phoelich CC, Wentwoord RA, Glandorf DC, Wijffelman CA, Lugtenberg BJ. Role of the O-antigen of lipopolysaccharide, and possible roles of growth rate and of NADH:ubiquinone oxidoreductase (nuo) in competitive tomato root-tip colonization by Pseudomonas fluorescens WCS365. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 1998; 11:763-771. [PMID: 9675892 DOI: 10.1094/mpmi.1998.11.8.763] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Colonization-defective, transposon-induced mutants of the efficient root colonizer Pseudomonas fluorescens WCS365 were identified with a gnotobiotic system. Most mutants were impaired in known colonization traits, i.e., prototrophy for amino acids, motility, and synthesis of the O-antigen of LPS (lipopolysaccharide). Mutants lacking the O-antigen of LPS were impaired in both colonization and competitive growth whereas one mutant (PCL1205) with a shorter O-antigen chain was defective only in colonization ability, suggesting a role for the intact O-antigen of LPS in colonization. Eight competitive colonization mutants that were not defective in the above-mentioned traits colonized the tomato root tip well when inoculated alone, but were defective in competitive root colonization of tomato, radish, and wheat, indicating they contained mutations affecting host range. One of these eight mutants (PCL1201) was further characterized and contains a mutation in a gene that shows homology to the Escherichia coli nuo4 gene, which encodes a subunit of one of two known NADH:ubiquinone oxidoreductases. Competition experiments in an oxygen-poor medium between mutant PCL1201 and its parental strain showed a decreased growth rate of mutant PCL1201. The requirement of the nuo4 gene homolog for optimal growth under conditions of oxygen limitation suggests that the root-tip environment is micro-aerobic. A mutant characterized by a slow growth rate (PCL1216) was analyzed further and contained a mutation in a gene with similarity to the E. coli HtrB protein, a lauroyl transferase that functions in lipid A biosynthesis.
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Affiliation(s)
- L C Dekkers
- Leiden University, Institute of Molecular Plant Sciences, Clusius Laboratory, The Netherlands.
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38
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van de Guchte M, Ehrlich DS, Chopin A. tRNATrp as a key element of antitermination in the Lactococcus lactis trp operon. Mol Microbiol 1998; 29:61-74. [PMID: 9701803 DOI: 10.1046/j.1365-2958.1998.00903.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The expression of the trp operon of Lactococcus lactis is regulated in response to tryptophan availability by a mechanism of transcription antitermination. We present evidence in support of a previously described model involving tRNATrp as a key element in the sensing of tryptophan levels and the realization of the regulatory response to tryptophan limitation. In agreement with this model, two sites of presumed direct interaction between the trp leader transcript and tRNATrp are found to be of crucial importance for efficient antitermination. These correspond to the specifier codon, which presumably interacts with the anticodon in the tRNA, and a sequence complementary to, and presumably interacting with, the acceptor stem of the tRNA. Through these interactions, uncharged tRNATrp is believed to stabilize an antiterminator conformation of the trp leader transcript, thus allowing transcription and expression of the structural genes of the operon. For the first time, we present direct evidence that it is the ratio of uncharged to charged tRNA that is important for the regulation of antitermination, rather than the absolute amount of uncharged tRNA. In addition, our results indicate that the codon-anticodon interaction, although contributing largely to the efficiency of the regulatory response, is not strictly indispensable, which suggests the existence of additional interactions between mRNA and tRNA. Finally, we describe a possible additional level of regulation, superimposed and dependent on tRNA-mediated anti-termination control, that is based on the processing of the trp leader transcript. Together with the regulation mechanisms described earlier for the Escherichia coli and Bacillus subtilis trp operons, this constitutes the third different mechanism of transcript elongation control found to be involved in the regulation of an operon of which the structural genes are highly conserved.
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Affiliation(s)
- M van de Guchte
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy-en-Josas, France.
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39
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Brandsma M, Janssen GM, Möller W. Termination of quiescence in crustacea. The role of transfer RNA aminoacylation in the brine shrimp Artemia. J Biol Chem 1997; 272:28912-7. [PMID: 9360961 DOI: 10.1074/jbc.272.46.28912] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In quiescent embryos of the brine shrimp Artemia, the level of aminoacylation of transfer RNAs is low. During resumption of development the charging level of transfer RNAs increases, concomitant with the activation of protein synthesis. The total level of charging rises dramatically from an average of 4% to 50% within a period of 24 h of development. The restriction of in vitro translation of the quiescent embryo extract can be partially released by the addition of charged aminoacyl-tRNA, which apparently starts the flow of ribosomes into polyribosome structures. Complete reactivation of translation by aminoacyl-tRNA occurs when mRNA from preformed mRNA-ribosome complexes, like the polyribosomes extracted from developing embryos or poly(U)-programmed ribosomes, are offered to quiescent embryo extracts. With respect to the mechanism of in vivo recharging of tRNAs, we observed that the level of several aminoacyl-tRNA synthetases increase during development. Methionyl-tRNA synthetase rises more than 10-fold. In the case of valyl-tRNA synthetase, the activation is lower and shown to be due to the de novo synthesis of its mRNA and the corresponding protein product as well. We conclude that protein synthesis and thereby the gradual animation of cryptobiotic Artemia embryos is determined to a large extent by the rate by which aminoacyl-tRNAs are replenished during development at both the initiation and elongation level.
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Affiliation(s)
- M Brandsma
- Department of Medical Biochemistry, Leiden University, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
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40
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Grundy FJ, Haldeman MT, Hornblow GM, Ward JM, Chalker AF, Henkin TM. The Staphylococcus aureus ileS gene, encoding isoleucyl-tRNA synthetase, is a member of the T-box family. J Bacteriol 1997; 179:3767-72. [PMID: 9171428 PMCID: PMC179176 DOI: 10.1128/jb.179.11.3767-3772.1997] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Staphylococcus aureus ileS gene, encoding isoleucyl-tRNA synthetase (IleRS), contains a long mRNA leader region. This region exhibits many of the features of the gram-positive synthetase gene family, including the T box and leader region terminator and antiterminator. The terminator was shown to be functional in vivo, and readthrough increased during growth in the presence of mupirocin, an inhibitor of IleRS activity. The S. aureus ileS leader structure includes several critical differences from the other members of the T-box family, suggesting that regulation of this gene in S. aureus may exhibit unique features.
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Affiliation(s)
- F J Grundy
- Department of Microbiology, Ohio State University, Columbus 43210, USA
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41
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Condon C, Putzer H, Luo D, Grunberg-Manago M. Processing of the Bacillus subtilis thrS leader mRNA is RNase E-dependent in Escherichia coli. J Mol Biol 1997; 268:235-42. [PMID: 9159466 DOI: 10.1006/jmbi.1997.0971] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have recently reported that processing occurs in the untranslated leader region of several members of a family of Gram-positive genes regulated by tRNA-mediated antitermination. We showed that cleavage at this site plays an important role in the induction of Bacillus subtilis thrS gene expression, following threonine starvation, by stabilising the downstream mRNA. Here we show that, when transferred on a plasmid, processing of the B. subtilis thrS leader can occur at the same site in Escherichia coli. Cleavage at this site is dependent on the E. coli endoribonuclease E, both in vivo and in vitro, suggesting that a functional homologue of RNase E is responsible for thrS processing in B. subtilis.
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Affiliation(s)
- C Condon
- UPR 9073, Institut de Biologie Physico-Chimique, Paris, France
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42
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Grundy FJ, Hodil SE, Rollins SM, Henkin TM. Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination. J Bacteriol 1997; 179:2587-94. [PMID: 9098057 PMCID: PMC179008 DOI: 10.1128/jb.179.8.2587-2594.1997] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Bacillus subtilis tyrS gene, encoding tyrosyl-tRNA synthetase, is a member of the T-box family of genes, which are regulated by control of readthrough of a leader region transcriptional terminator. Readthrough is induced by interaction of the cognate uncharged tRNA with the leader; the system responds to decreased tRNA charging, caused by amino acid limitation or insufficient levels of the aminoacyl-tRNA synthetase. Recognition of the cognate tRNA is mediated by pairing of the anticodon of the tRNA with the specifier sequence of the leader, a codon specifying the appropriate amino acid; a second interaction between the acceptor end of the tRNA and an antiterminator structure is also important. Certain switches of the specifier sequence to a new codon result in a switch in the specificity of the amino acid response, while other switches do not. These effects may reflect additional sequence or structural requirements for the mRNA-tRNA interaction. This study includes investigation of the effects of a large number of specifier sequence switches in tyrS and analysis of structural differences between tRNA(Tyr) and tRNA species which interact inefficiently with the tyrS leader to promote antitermination.
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MESH Headings
- Bacillus subtilis/genetics
- Base Sequence
- Codon/genetics
- Gene Expression Regulation, Bacterial/genetics
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Transfer/genetics
- RNA, Transfer, Thr/genetics
- RNA, Transfer, Tyr/genetics
- Tyrosine-tRNA Ligase/genetics
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Affiliation(s)
- F J Grundy
- Department of Microbiology, The Ohio State University, Columbus 43210, USA
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43
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Luo D, Leautey J, Grunberg-Manago M, Putzer H. Structure and regulation of expression of the Bacillus subtilis valyl-tRNA synthetase gene. J Bacteriol 1997; 179:2472-8. [PMID: 9098041 PMCID: PMC178992 DOI: 10.1128/jb.179.8.2472-2478.1997] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have sequenced the valyl-tRNA synthetase gene (valS) of Bacillus subtilis and found an open reading frame coding for a protein of 880 amino acids with a molar mass of 101,749. The predicted amino acid sequence shares strong similarity with the valyl-tRNA synthetases from Bacillus stearothermophilus, Lactobacillus casei, and Escherichia coli. Extracts of B. subtilis strains overexpressing the valS gene on a plasmid have increased valyl-tRNA aminoacylation activity. Northern analysis shows that valS is cotranscribed with the folC gene (encoding folyl-polyglutamate synthetase) lying downstream. The 300-bp 5' noncoding region of the gene contains the characteristic regulatory elements, T box, "specifier codon" (GUC), and rho-independant transcription terminator of a gene family in gram-positive bacteria that encodes many aminoacyl-tRNA synthetases and some amino acid biosynthetic enzymes and that is regulated by tRNA-mediated antitermination. We have shown that valS expression is induced by valine limitation and that the specificity of induction can be switched to threonine by changing the GUC (Val) specifier triplet to ACC (Thr). Overexpression of valS from a recombinant plasmid leads to autorepression of a valS-lacZ transcriptional fusion. Like induction by valine starvation, autoregulation of valS depends on the presence of the GUC specifier codon. Disruption of the valS gene was not lethal, suggesting the existence of a second gene, as is the case for both the thrS and the tyrS genes.
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MESH Headings
- Acylation
- Amino Acid Sequence
- Bacillus subtilis/enzymology
- Bacillus subtilis/genetics
- Base Sequence
- Chromosome Mapping
- DNA, Recombinant
- Escherichia coli/genetics
- Gene Expression Regulation, Bacterial/physiology
- Genes, Bacterial/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Open Reading Frames
- Peptide Synthases/genetics
- RNA, Bacterial/analysis
- RNA, Bacterial/chemistry
- RNA, Messenger/analysis
- RNA, Messenger/chemistry
- RNA, Transfer, Val/metabolism
- Regulatory Sequences, Nucleic Acid/genetics
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Transcription, Genetic/genetics
- Valine-tRNA Ligase/genetics
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Affiliation(s)
- D Luo
- UPR 9073, CNRS, Institut de Biologie Physico-Chimique, Paris, France
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44
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Abstract
A growing number of genetic systems have been shown to be controlled at the level of premature termination of transcription. Genes in this class contain transcription termination signals in the region upstream of the coding sequence. The activity of these regulatory termination signals is controlled through a variety of mechanisms. These include modification of RNA polymerase to a terminator-resistant, or terminator-prone form, and alterations in the structure of the nascent transcript, to determine whether the stem-loop structure of an intrinsic terminator or an alternate antiterminator is formed. Structural alterations in the transcript can be controlled by the kinetics of translation of the RNA, by binding of specific regulatory proteins, and by mRNA-tRNA interactions. This review describes a number of variations on the termination control theme that have been uncovered in prokaryotes.
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Affiliation(s)
- T M Henkin
- Department of Microbiology, Ohio State University, Columbus 43210, USA
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45
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Condon C, Putzer H, Grunberg-Manago M. Processing of the leader mRNA plays a major role in the induction of thrS expression following threonine starvation in Bacillus subtilis. Proc Natl Acad Sci U S A 1996; 93:6992-7. [PMID: 8692931 PMCID: PMC38922 DOI: 10.1073/pnas.93.14.6992] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The threonyl-tRNA synthetase gene, thrS, is a member of a family of Gram-positive genes that are induced following starvation for the corresponding amino acid by a transcriptional antitermination mechanism involving the cognate uncharged tRNA. Here we show that an additional level of complexity exists in the control of the thrS gene with the mapping of an mRNA processing site just upstream of the transcription terminator in the thrS leader region. The processed RNA is significantly more stable than the full-length transcript. Under nonstarvation conditions, or following starvation for an amino acid other than threonine, the full-length thrS mRNA is more abundant than the processed transcript. However, following starvation for threonine, the thrS mRNA exists primarily in its cleaved form. This can partly be attributed to an increased processing efficiency following threonine starvation, and partly to a further, nonspecific increase in the stability of the processed transcript under starvation conditions. The increased stability of the processed RNA contributes significantly to the levels of functional RNA observed under threonine starvation conditions, previously attributed solely to antitermination. Finally, we show that processing is likely to occur upstream of the terminator in the leader regions of at least four other genes of this family, suggesting a widespread conservation of this phenomenon in their control.
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Affiliation(s)
- C Condon
- Unité Propre de Recherche 9073, Institut de Biologie Physic-Chimique, Paris, France
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46
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Marta PT, Ladner RD, Grandoni JA. A CUC triplet confers leucine-dependent regulation of the Bacillus subtilis ilv-leu operon. J Bacteriol 1996; 178:2150-3. [PMID: 8606198 PMCID: PMC177919 DOI: 10.1128/jb.178.7.2150-2153.1996] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Regulation of the ilv-leu operon probably involves interaction of a tR NA(GAG) with leader region mRNA. Conversion of a CUC (Leu) triplet located within the leader region to UUC (Phe), CGC (Arg), or UAC (Tyr) converted reporter gene expression to control by corresponding amino acids. Conversion of the CUC triplet to CUU (Leu) decreased expression and disrupted regulation. The results suggested that other tRNAs can substitute for tRNA(Leu) but that interactions in addition to pairing of the anticodon with the CUC triplet are important for proper control.
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Affiliation(s)
- P T Marta
- Department of Molecular Biology, University of Medicine and Dentistry of New Jersey School of Osteopathic Medicine, Stratford, New Jersey 08084, USA
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47
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Abstract
In this review, we summarize progress on the regulation of the aminoacyl-tRNA synthetase genes in Bacillus subtilis. Most of the genes encoding this set of enzymes in B subtilis are members of a large family of Gram-positive genes and operons controlled by a novel antitermination mechanism that uses their cognate uncharged tRNA as the effector. A subset of these genes is, in addition, likely to be controlled at the level of mRNA processing and degradation. We describe the key experiments leading to these conclusions.
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Affiliation(s)
- C Condon
- UPR 9073, Institut de Biologie Physico-Chimique, Paris, France
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